fifteen garlic genotypes were collected from different regions of Delta and cultivated in new reclaimed sandy loam soil over two seasons (2022 and 2023). The selection of garlic clones and strains with genetic traits that facilitate adaptation to fluctuating and unpredictable environmental conditions is of utmost importance. Also protecting agricultural genetic resources is a paramount responsibility. Molecular genetic markers have emerged as a crucial contemporary method for assessing genetic diversity and enhancing agricultural yield in breeding programs. In this regard, SRAP (sequence-related amplified polymorphism) and SCoT (start codon targeted) markers were employed to evaluate the genetic variation and relationships among the garlic genotypes. Results of the morphological analysis revealed significant variations in all the investigated traits. Genotypes 1 and 7 exhibited superiority over other genotypes in certain morphological features, such as bulb weight, bulb height, and yield. Furthermore, the SRAP and SCoT markers demonstrated a high level of genetic variation among the garlic genotypes. Notably, several positive and negative markers associated with bulb weight and yield traits were identified using the SRAP and SCoT markers. At the molecular marker level, our findings indicated that the G2 genotype displayed superior yields and weights compared to its origin genotype, G5, and exhibited genetic differentiation and independence in a distinct clade. This suggests that new garlic varieties can be genetically enhanced by leveraging the genes present in this particular genotype